Literature DB >> 25215768

Defining the free-energy landscape of curvature-inducing proteins on membrane bilayers.

Richard W Tourdot1, N Ramakrishnan2, Ravi Radhakrishnan3.   

Abstract

Curvature-sensing and curvature-remodeling proteins, such as Amphiphysin, Epsin, and Exo70, are known to reshape cell membranes, and this remodeling event is essential for key biophysical processes such as tubulation, exocytosis, and endocytosis. Curvature-inducing proteins can act as curvature sensors; they aggregate to membrane regions matching their intrinsic curvature; as well as induce curvature in cell membranes to stabilize emergent high curvature, nonspherical, structures such as tubules, discs, and caveolae. A definitive understanding of the interplay between protein recruitment and migration, the evolution of membrane curvature, and membrane morphological transitions is emerging but remains incomplete. Here, within a continuum framework and using the machinery of Monte Carlo simulations, we introduce and compare three free-energy methods to delineate the free-energy landscape of curvature-inducing proteins on bilayer membranes. We demonstrate the utility of the Widom test particle (or field) insertion methodology in computing the excess chemical potentials associated with curvature-inducing proteins on the membrane-in particular, we use this method to track the onset of morphological transitions in the membrane at elevated protein densities. We validate this approach by comparing the results from the Widom method with those of thermodynamic integration and Bennett acceptance ratio methods. Furthermore, the predictions from the Widom method have been tested against analytical calculations of the excess chemical potential at infinite dilution. Our results are useful in precisely quantifying the free-energy landscape, and also in determining the phase boundaries associated with curvature-induction, curvature-sensing, and morphological transitions. This approach can be extended to studies exploring the role of thermal fluctuations and other external (control) variables, such as membrane excess area, in shaping curvature-mediated interactions on bilayer membranes.

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Year:  2014        PMID: 25215768      PMCID: PMC4336182          DOI: 10.1103/PhysRevE.90.022717

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  49 in total

1.  Nonlinear sorting, curvature generation, and crowding of endophilin N-BAR on tubular membranes.

Authors:  Chen Zhu; Sovan L Das; Tobias Baumgart
Journal:  Biophys J       Date:  2012-04-18       Impact factor: 4.033

2.  Curvature-induced lateral phase segregation in two-component vesicles.

Authors: 
Journal:  Phys Rev Lett       Date:  1993-03-01       Impact factor: 9.161

Review 3.  Membrane curvature and mechanisms of dynamic cell membrane remodelling.

Authors:  Harvey T McMahon; Jennifer L Gallop
Journal:  Nature       Date:  2005-12-01       Impact factor: 49.962

4.  Interaction between inclusions embedded in membranes.

Authors:  H Aranda-Espinoza; A Berman; N Dan; P Pincus; S Safran
Journal:  Biophys J       Date:  1996-08       Impact factor: 4.033

Review 5.  Continuum simulations of biomembrane dynamics and the importance of hydrodynamic effects.

Authors:  Frank L H Brown
Journal:  Q Rev Biophys       Date:  2011-07-01       Impact factor: 5.318

6.  Comparison of thermodynamic integration and Bennett acceptance ratio for calculating relative protein-ligand binding free energies.

Authors:  Anita de Ruiter; Stefan Boresch; Chris Oostenbrink
Journal:  J Comput Chem       Date:  2013-01-19       Impact factor: 3.376

7.  Dynamic sorting of lipids and proteins in membrane tubes with a moving phase boundary.

Authors:  Michael Heinrich; Aiwei Tian; Cinzia Esposito; Tobias Baumgart
Journal:  Proc Natl Acad Sci U S A       Date:  2010-04-05       Impact factor: 11.205

Review 8.  Thermodynamics and mechanics of membrane curvature generation and sensing by proteins and lipids.

Authors:  Tobias Baumgart; Benjamin R Capraro; Chen Zhu; Sovan L Das
Journal:  Annu Rev Phys Chem       Date:  2011       Impact factor: 12.703

9.  Sorting of lipids and proteins in membrane curvature gradients.

Authors:  A Tian; T Baumgart
Journal:  Biophys J       Date:  2009-04-08       Impact factor: 4.033

10.  Multiscale computational models in physical systems biology of intracellular trafficking.

Authors:  Richard W Tourdot; Ryan P Bradley; Natesan Ramakrishnan; Ravi Radhakrishnan
Journal:  IET Syst Biol       Date:  2014-10       Impact factor: 1.615

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  12 in total

1.  Application of a free-energy-landscape approach to study tension-dependent bilayer tubulation mediated by curvature-inducing proteins.

Authors:  Richard W Tourdot; N Ramakrishnan; Tobias Baumgart; Ravi Radhakrishnan
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2015-10-29

2.  Mesoscale computational studies of membrane bilayer remodeling by curvature-inducing proteins.

Authors:  N Ramakrishnan; P B Sunil Kumar; Ravi Radhakrishnan
Journal:  Phys Rep       Date:  2014-10-01       Impact factor: 25.600

3.  Membrane Morphologies Induced by Arc-Shaped Scaffolds Are Determined by Arc Angle and Coverage.

Authors:  Francesco Bonazzi; Thomas R Weikl
Journal:  Biophys J       Date:  2019-02-26       Impact factor: 4.033

4.  Curvature-undulation coupling as a basis for curvature sensing and generation in bilayer membranes.

Authors:  Ryan P Bradley; Ravi Radhakrishnan
Journal:  Proc Natl Acad Sci U S A       Date:  2016-08-16       Impact factor: 11.205

5.  Phenomenology based multiscale models as tools to understand cell membrane and organelle morphologies.

Authors:  N Ramakrishnan; Ravi Radhakrishnan
Journal:  Adv Planar Lipid Bilayers Liposomes       Date:  2015

6.  Biophysics of membrane curvature remodeling at molecular and mesoscopic lengthscales.

Authors:  N Ramakrishnan; Ryan P Bradley; Richard W Tourdot; Ravi Radhakrishnan
Journal:  J Phys Condens Matter       Date:  2018-05-22       Impact factor: 2.333

7.  ECM dimensionality tunes actin tension to modulate endoplasmic reticulum function and spheroid phenotypes of mammary epithelial cells.

Authors:  FuiBoon Kai; Guanqing Ou; Richard W Tourdot; Connor Stashko; Guido Gaietta; Mark F Swift; Niels Volkmann; Alexandra F Long; Yulong Han; Hector H Huang; Jason J Northey; Andrew M Leidal; Virgile Viasnoff; David M Bryant; Wei Guo; Arun P Wiita; Ming Guo; Sophie Dumont; Dorit Hanein; Ravi Radhakrishnan; Valerie M Weaver
Journal:  EMBO J       Date:  2022-07-25       Impact factor: 14.012

8.  Excess area dependent scaling behavior of nano-sized membrane tethers.

Authors:  N Ramakrishnan; K K Sreeja; Arpita Roychoudhury; David M Eckmann; Portonovo S Ayyaswamy; Tobias Baumgart; Thomas Pucadyil; Shivprasad Patil; Valerie M Weaver; Ravi Radhakrishnan
Journal:  Phys Biol       Date:  2018-01-11       Impact factor: 2.583

9.  Thermodynamic free energy methods to investigate shape transitions in bilayer membranes.

Authors:  N Ramakrishnan; Richard W Tourdot; Ravi Radhakrishnan
Journal:  Int J Adv Eng Sci Appl Math       Date:  2016-01-22

10.  Multiscale computational models in physical systems biology of intracellular trafficking.

Authors:  Richard W Tourdot; Ryan P Bradley; Natesan Ramakrishnan; Ravi Radhakrishnan
Journal:  IET Syst Biol       Date:  2014-10       Impact factor: 1.615

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